Merge pull request #35 from noaa-ocs-modeling/develop

update examples, use `appdirs` for downloading TPXO dataset, use newer version of `adcircpy`

coupledmodeldriver/adcirc.py

@@ -18,7 +18,7 @@
     RunScript,
     SlurmEmailType,
 )
-from .utilities import get_logger
+from .utilities import create_symlink, get_logger
 
 LOGGER = get_logger('adcirc')
 
@@ -113,11 +113,19 @@ def write_adcirc_configurations(
             output_directory, overwrite=overwrite, include_version=True
         )
 
-    for filename in coldstart_filenames + [atm_namelist_filename]:
+    coldstart_filenames.append(atm_namelist_filename)
+    for filename in coldstart_filenames:
         coldstart_filename = Path(f'{filename}.coldstart')
         if coldstart_filename.exists():
             os.remove(coldstart_filename)
-        filename.rename(coldstart_filename)
+        if filename.is_symlink():
+            target = filename.resolve()
+            if target in coldstart_filenames:
+                target = f'{target}.coldstart'
+            create_symlink(target, coldstart_filename)
+            os.remove(filename)
+        else:
+            filename.rename(coldstart_filename)
 
     if spinup is not None:
         hotstart_filenames = nems.write(
@@ -127,10 +135,17 @@ def write_adcirc_configurations(
         hotstart_filenames = []
 
     for filename in hotstart_filenames + [atm_namelist_filename]:
-        coldstart_filename = Path(f'{filename}.hotstart')
-        if coldstart_filename.exists():
-            os.remove(coldstart_filename)
-        filename.rename(coldstart_filename)
+        hotstart_filename = Path(f'{filename}.hotstart')
+        if hotstart_filename.exists():
+            os.remove(hotstart_filename)
+        if filename.is_symlink():
+            target = filename.resolve()
+            if target in hotstart_filenames:
+                target = f'{target}.coldstart'
+            create_symlink(target, hotstart_filename)
+            os.remove(filename)
+        else:
+            filename.rename(hotstart_filename)
 
     coldstart_directory = output_directory / 'coldstart'
     runs_directory = output_directory / 'runs'

coupledmodeldriver/job_script.py

@@ -323,7 +323,7 @@ def __init__(
 
         if self.fort67_filename is not None:
             self.commands.extend(
-                [f'ln -sf {self.fort67_filename} ./fort.67.nc', '', ]
+                [f'ln -sf {self.fort67_filename} ./fort.67.nc', '']
             )
 
         self.commands.append(f'{self.launcher} {self.nems_path}')
@@ -408,7 +408,7 @@ def __str__(self) -> str:
             '# run every hotstart configuration',
             bash_for_loop(
                 'for hotstart in $DIRECTORY/runs/*/',
-                ['cd "$hotstart"', self.hotstart, 'cd $DIRECTORY', ],
+                ['cd "$hotstart"', self.hotstart, 'cd $DIRECTORY'],
             ),
         ]
 
@@ -441,7 +441,7 @@ def coldstart(self) -> str:
             )
         else:
             lines.extend(
-                ['sh adcprep.job', 'sh nems_adcirc.job', ]
+                ['sh adcprep.job', 'sh nems_adcirc.job']
             )
         return '\n'.join(lines)
 
@@ -457,7 +457,7 @@ def hotstart(self) -> str:
             )
         else:
             lines.extend(
-                ['sh adcprep.job', 'sh nems_adcirc.job', ]
+                ['sh adcprep.job', 'sh nems_adcirc.job']
             )
         return '\n'.join(lines)
 

coupledmodeldriver/utilities.py

@@ -80,20 +80,21 @@ def filter(self, rec):
 LOGGER = get_logger('utilities')
 
 
-def create_symlink(from_filename: PathLike, to_filename: PathLike, overwrite: bool = False):
-    if not isinstance(from_filename, Path):
-        from_filename = Path(from_filename)
-    if not isinstance(to_filename, Path):
-        to_filename = Path(to_filename)
+def create_symlink(source_filename: PathLike, symlink_filename: PathLike):
+    if not isinstance(source_filename, Path):
+        source_filename = Path(source_filename)
+    if not isinstance(symlink_filename, Path):
+        symlink_filename = Path(symlink_filename)
 
-    if to_filename.exists() and overwrite:
-        os.remove(to_filename)
+    if symlink_filename.is_symlink():
+        LOGGER.debug(f'removing symlink {symlink_filename}')
+        os.remove(symlink_filename)
 
     try:
-        to_filename.symlink_to(from_filename)
+        symlink_filename.symlink_to(source_filename)
     except Exception as error:
         LOGGER.warning(f'could not create symbolic link: {error}')
-        shutil.copyfile(from_filename, to_filename)
+        shutil.copyfile(source_filename, symlink_filename)
 
 
 def ellipsoidal_distance(

examples/hera/hera_hsofs_irma.py

@@ -5,6 +5,7 @@
 import sys
 
 from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
@@ -28,6 +29,8 @@
 # directory to which to write configuration
 OUTPUT_DIRECTORY = Path(__file__).parent.parent / 'data' / 'configuration' / 'hera_hsofs_irma'
 
+HAMTIDE_DIRECTORY = '/scratch2/COASTAL/coastal/save/shared/models/forcings/tides/hamtide'
+
 if __name__ == '__main__':
     # dictionary defining runs with ADCIRC value perturbations - in this case, a single run with no perturbation
     runs = {f'test_case_1': (None, None)}
@@ -56,7 +59,7 @@
     ]
 
     # initialize `adcircpy` forcing objects
-    tidal_forcing = Tides()
+    tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=HAMTIDE_DIRECTORY)
     tidal_forcing.use_all()
     wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
     wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)

examples/hera/hera_hsofs_sandy.py

@@ -5,6 +5,7 @@
 import sys
 
 from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
@@ -28,6 +29,8 @@
 # directory to which to write configuration
 OUTPUT_DIRECTORY = Path(__file__).parent.parent / 'data' / 'configuration' / 'hera_hsofs_sandy'
 
+HAMTIDE_DIRECTORY = '/scratch2/COASTAL/coastal/save/shared/models/forcings/tides/hamtide'
+
 if __name__ == '__main__':
     # dictionary defining runs with ADCIRC value perturbations - in this case, a single run with no perturbation
     runs = {f'test_case_1': (None, None)}
@@ -56,7 +59,7 @@
     ]
 
     # initialize `adcircpy` forcing objects
-    tidal_forcing = Tides()
+    tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=HAMTIDE_DIRECTORY)
     tidal_forcing.use_all()
     wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
     wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)

examples/hera/hera_shinnecock_ike.py

@@ -5,6 +5,7 @@
 import sys
 
 from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
@@ -30,6 +31,8 @@
     Path(__file__).parent.parent / 'data' / 'configuration' / 'hera_shinnecock_ike'
 )
 
+HAMTIDE_DIRECTORY = '/scratch2/COASTAL/coastal/save/shared/models/forcings/tides/hamtide'
+
 if __name__ == '__main__':
     # dictionary defining runs with ADCIRC value perturbations - in this case, a single run with no perturbation
     runs = {f'test_case_1': (None, None)}
@@ -60,7 +63,7 @@
     ]
 
     # initialize `adcircpy` forcing objects
-    tidal_forcing = Tides()
+    tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=HAMTIDE_DIRECTORY)
     tidal_forcing.use_all()
     wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
     wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)

examples/hera/hera_shinnecock_ike_perturbed_mannings_n.py

@@ -5,6 +5,7 @@
 import sys
 
 from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
@@ -34,6 +35,8 @@
     / 'hera_shinnecock_ike_perturbed_mannings_n'
 )
 
+HAMTIDE_DIRECTORY = '/scratch2/COASTAL/coastal/save/shared/models/forcings/tides/hamtide'
+
 if __name__ == '__main__':
     # dictionary defining runs with ADCIRC value perturbations - in this case, a range of Manning's N values
     range = [0.016, 0.08]
@@ -67,7 +70,7 @@
     ]
 
     # initialize `adcircpy` forcing objects
-    tidal_forcing = Tides()
+    tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=HAMTIDE_DIRECTORY)
     tidal_forcing.use_all()
     wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
     wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)

examples/local/local_hsofs_irma.py

@@ -5,6 +5,7 @@
 import sys
 
 from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
@@ -17,7 +18,7 @@
 
 # directory containing input ADCIRC mesh nodes (`fort.14`) and (optionally) mesh values (`fort.13`)
 MESH_DIRECTORY = (
-    Path(__file__).parent.parent / 'data' / 'input' / 'meshes' / 'hsofs' / 'irma' / 'grid_v1'
+    Path(__file__).parent.parent / 'data' / 'input' / 'meshes' / 'hsofs' / 'grid_v1'
 )
 
 # directory containing input atmospheric mesh forcings (`wind_atm_fin_ch_time_vec.nc`) and WaveWatch III forcings (`ww3.Constant.20151214_sxy_ike_date.nc`)
@@ -56,7 +57,7 @@
     ]
 
     # initialize `adcircpy` forcing objects
-    tidal_forcing = Tides()
+    tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=None)
     tidal_forcing.use_all()
     wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
     wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)

examples/local/local_hsofs_sandy.py

@@ -5,6 +5,7 @@
 import sys
 
 from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
@@ -17,7 +18,7 @@
 
 # directory containing input ADCIRC mesh nodes (`fort.14`) and (optionally) mesh values (`fort.13`)
 MESH_DIRECTORY = (
-    Path(__file__).parent.parent / 'data' / 'input' / 'meshes' / 'hsofs' / 'sandy' / 'grid_v1'
+    Path(__file__).parent.parent / 'data' / 'input' / 'meshes' / 'hsofs' / 'grid_v1'
 )
 
 # directory containing input atmospheric mesh forcings (`wind_atm_fin_ch_time_vec.nc`) and WaveWatch III forcings (`ww3.Constant.20151214_sxy_ike_date.nc`)
@@ -56,7 +57,7 @@
     ]
 
     # initialize `adcircpy` forcing objects
-    tidal_forcing = Tides()
+    tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=None)
     tidal_forcing.use_all()
     wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
     wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)

examples/local/local_shinnecock_ike.py

@@ -5,6 +5,7 @@
 import sys
 
 from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
@@ -17,13 +18,7 @@
 
 # directory containing input ADCIRC mesh nodes (`fort.14`) and (optionally) mesh values (`fort.13`)
 MESH_DIRECTORY = (
-    Path(__file__).parent.parent
-    / 'data'
-    / 'input'
-    / 'meshes'
-    / 'shinnecock'
-    / 'ike'
-    / 'grid_v1'
+    Path(__file__).parent.parent / 'data' / 'input' / 'meshes' / 'shinnecock' / 'grid_v1'
 )
 
 # directory containing input atmospheric mesh forcings (`wind_atm_fin_ch_time_vec.nc`) and WaveWatch III forcings (`ww3.Constant.20151214_sxy_ike_date.nc`)
@@ -62,7 +57,7 @@
     ]
 
     # initialize `adcircpy` forcing objects
-    tidal_forcing = Tides()
+    tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=None)
     tidal_forcing.use_all()
     wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
     wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)

examples/local/local_shinnecock_ike_perturbed_mannings_n.py

@@ -5,6 +5,7 @@
 import sys
 
 from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
@@ -18,13 +19,7 @@
 
 # directory containing input ADCIRC mesh nodes (`fort.14`) and (optionally) mesh values (`fort.13`)
 MESH_DIRECTORY = (
-    Path(__file__).parent.parent
-    / 'data'
-    / 'input'
-    / 'meshes'
-    / 'shinnecock'
-    / 'ike'
-    / 'grid_v1'
+    Path(__file__).parent.parent / 'data' / 'input' / 'meshes' / 'shinnecock' / 'grid_v1'
 )
 
 # directory containing input atmospheric mesh forcings (`wind_atm_fin_ch_time_vec.nc`) and WaveWatch III forcings (`ww3.Constant.20151214_sxy_ike_date.nc`)
@@ -73,7 +68,7 @@
     ]
 
     # initialize `adcircpy` forcing objects
-    tidal_forcing = Tides()
+    tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=None)
     tidal_forcing.use_all()
     wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
     wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)

examples/stampede2/stampede2_hsofs_sandy.py

@@ -5,6 +5,7 @@
 import sys
 
 from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
@@ -52,7 +53,7 @@
     ]
 
     # initialize `adcircpy` forcing objects
-    tidal_forcing = Tides()
+    tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=None)
     tidal_forcing.use_all()
     wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
     wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)

examples/stampede2/stampede2_shinnecock_ike.py

@@ -5,6 +5,7 @@
 import sys
 
 from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
@@ -54,7 +55,7 @@
     ]
 
     # initialize `adcircpy` forcing objects
-    tidal_forcing = Tides()
+    tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=None)
     tidal_forcing.use_all()
     wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
     wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)

examples/stampede2/stampede2_shinnecock_ike_perturbed_mannings_n.py

@@ -5,6 +5,7 @@
 import sys
 
 from adcircpy import Tides
+from adcircpy.forcing.tides.tides import TidalSource
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
 from nemspy import ModelingSystem
@@ -62,7 +63,7 @@
     ]
 
     # initialize `adcircpy` forcing objects
-    tidal_forcing = Tides()
+    tidal_forcing = Tides(tidal_source=TidalSource.HAMTIDE, resource=None)
     tidal_forcing.use_all()
     wind_forcing = AtmosphericMeshForcing(nws=17, interval_seconds=3600)
     wave_forcing = WaveWatch3DataForcing(nrs=5, interval_seconds=3600)

setup.py

@@ -50,6 +50,6 @@
     packages=find_packages(),
     python_requires='>=3.6',
     setup_requires=['dunamai', 'setuptools>=41.2'],
-    install_requires=['adcircpy==1.0.20', 'nemspy>=0.6.2', 'numpy', 'requests'],
+    install_requires=['adcircpy>=1.0.21', 'nemspy>=0.6.5', 'numpy', 'requests'],
     extras_require={'testing': ['flake8', 'pytest', 'pytest-cov'], 'development': ['oitnb']},
 )